spm_mf_box.m

toolbox for spm 5 for data, model free analysis

else, return;
end
clear tm

handles.mfbss.name = cmd_algo;

handles.mfbss.reliability = struct();

if (isstruct(handles.mfbss.X)) % get real data + reduce size
    if (all(handles.mfbss.mask(:)))
        handles.mfbss.X = single(mfbox_databackend('getdata',handles.mfbss.X));
    else
        X = handles.mfbss.X;
        m = sum(handles.mfbss.mask(:));
        handles.mfbss.X = zeros(m,X.timesteps,'single');
        for i=1:X.timesteps
            v = reshape(mfbox_databackend('getdata',X,i),[],1);
            handles.mfbss.X(:,i) = v(handles.mfbss.mask);
        end
    end
    handles.mfbss.grid = handles.mfbss.grid(:,handles.mfbss.mask);
else
    sgr = size(handles.mfbss.grid);
    sm = size(handles.mfbss.mask);
    g = mat2cell(min(repmat(sm',1,sgr(2)),max(ones(sgr), ...
        round(handles.mfbss.grid))),ones(1,sgr(1)),sgr(2));
    mask = handles.mfbss.mask(sub2ind(sm,g{:}));
    handles.mfbss.grid = handles.mfbss.grid(:,mask);
    if ((length(size(handles.mfbss.X))>2)||(~isa(handles.mfbss.X,'single')))
        handles.mfbss.X = reshape(single(handles.mfbss.X),[],length(handles.mfbss.timeline));
    end
    if (any(mask(:)==0)), handles.mfbss.X = handles.mfbss.X(mask,:); end
end

p = {};
if (isfield(handles.mfbss.rel_params,cmd_rel))
    p = handles.mfbss.rel_params.(cmd_rel);
end
cmd_func = str2func(sprintf('mfbox_rel_%s_run',cmd_rel));

[handles.mfbss,p] = cmd_func(handles.mfbss,p,1);
if (isstruct(p)), handles.mfbss.rel_params.(cmd_rel) = p;
else return;
end
handles.mfbss.rel_name = cmd_rel;

s = [size(handles.mfbss.S.dat,1),size(handles.mfbss.S.map,2)];
S = zeros(s);
for i=1:s(2)
    j = unique(handles.mfbss.S.map(:,i));
    S(:,i) = sum(handles.mfbss.S.dat(:,j),2)/length(j);
end

p = {1:s(2)};
if (isfield(handles.mfbss.S,'part')), p = handles.mfbss.S.part; end

handles.mfbss.crosstalk = updatecrosstalk(handles.mfbss.A,S,p);

handles.mfbss.reliability = updatereliability(handles.mfbss.reliability,handles.mfbss.A,S);

handles.mfbss.reliability = updatedesign(handles.mfbss.reliability, ...
    handles.mfbss.design,handles.mfbss.timeline,handles.mfbss.A);

handles.mfbss.reliability = updatereference(handles.mfbss.reliability, ...
    handles.mfbss.reference,S,handles.mfbss.grid(:,handles.mfbss.S.mask));

v = fieldnames(handles.mfbss.reliability);
for i=1:length(v)
    if (isempty(handles.mfbss.reliability.(v{i})))
        handles.mfbss.reliability = rmfield(handles.mfbss.reliability,v{i});
    end
end

handles = reset_views(handles);

guidata(hObject,handles);


% --- Executes on button press in import_ref.
function import_ref_Callback(hObject,eventdata,handles)

[handles.mfbss.reference,handles.reference_filename,handles.private] = ...
    mfbox_databackend('import_reference',handles.private,handles.reference_filename);

if ((isfield(handles.mfbss.S,'dat'))&&(~isempty(handles.mfbss.reference)))
    s = [size(handles.mfbss.S.dat,1),size(handles.mfbss.S.map,2)];
    S = zeros(s);
    for i=1:s(2)
        j = unique(handles.mfbss.S.map(:,i));
        S(:,i) = sum(handles.mfbss.S.dat(:,j),2)/length(j);
    end
    handles.mfbss.reliability = updatereference(handles.mfbss.reliability, ...
        handles.mfbss.reference,S,handles.mfbss.grid(:,handles.mfbss.S.mask));
else
    if (isfield(handles.mfbss.reliability,'reference'))
        handles.mfbss.reliability = rmfield(handles.mfbss.reliability,'reference');
    end
end

handles = reset_views(handles);

guidata(hObject,handles);


% --- Executes on button press in import_des.
function import_des_Callback(hObject,eventdata,handles)

[handles.mfbss.design,handles.design_filename] = ...
    mfbox_databackend('import_design',handles.design_filename);

if (~isempty(handles.mfbss.A))
    handles.mfbss.reliability = updatedesign(handles.mfbss.reliability, ...
        handles.mfbss.design,handles.mfbss.timeline,handles.mfbss.A);
elseif (isfield(handles.mfbss,'reliability'))
    if (isfield(handles.mfbss.reliability,'design'))
        handles.mfbss.reliability = rmfield(handles.mfbss.reliability,'design');
    end
end

handles = reset_views(handles);

guidata(hObject,handles);


% --- Executes on button press in import_bg.
function import_bg_Callback(hObject,eventdata,handles)

[handles.mfbss.bg,handles.private] = ...
    mfbox_databackend('import_bg',handles.private,'');

handles.private = mfbox_databackend('init',handles.private, ...
        struct('seq',handles.sequence,'bg',handles.mfbss.bg));
    
handles = reset_views(handles);

guidata(hObject,handles);


% ---
function rel=updatereliability(rel,tc,sm)
v = var(tc);
rel.variance = double(v/max(v(:)));
rel.temporalsparseness = zeros(1,length(v));
for i=1:size(tc,2)
    w = tc(:,i)-mean(tc(:,i)); w = w/sqrt(v(i));
    n = size(tc,1);
    rel.temporalsparseness(i) = (sqrt(n-1)./sum(abs(w))).^(1/2);
end
rel.spatialsparseness = zeros(1,size(sm,2));
for i=1:size(sm,2)
    v = sm(:,i)-mean(sm(:,i)); n = size(sm,2);
    rel.spatialsparseness(i) = (sqrt(n-1)./sum(abs(v))).^(1/6);
end


% ---
function ct=updatecrosstalk(tc,sm,p)

ct = zeros(size(tc,2));
for i=1:length(p)
    if (length(p{i})>1)
        [f,t] = mfbox_cumindependence(tc(:,p{i}));
        [f,s] = mfbox_cumindependence(sm(:,p{i}));
        t = triu(t,1); s = tril(s,-1);
        ct(p{i},p{i}) = t/max(t(:))+s/max(s(:));
    end
end
for i=2:length(p)
    [f,t] = mfbox_cumindependence(tc(:,p{i-1}),tc(:,p{i}));
    [f,s] = mfbox_cumindependence(sm(:,p{i}),sm(:,p{i-1}));
    ct(p{i-1},p{i}) = t/max(t(:));
    ct(p{i},p{i-1}) = s/max(s(:));
end


% ---
function rel=updatereference(rel,ref,sm,gr)

sr = size(ref);
if (isfield(rel,'reference'))
    rel = rmfield(rel,'reference');
end
if (sr(2)~=0)
    s = size(gr);
    g = mat2cell(gr,ones(1,s(1)),s(2));
    ref = reshape(interpn(ref,g{:},'nearest')>0.75,1,[]);
    m = mean(sm,1);
    for i=1:size(sm,2), sm(:,i) = sm(:,i)-m(i); end
    vsm = var(sm,0,1);
    s = false(size(sm));
    for i=1:size(sm,2), s(:,i) = (sm(:,i).^2)>(4*vsm(i)); end
    [ci,rel.reference] = mfbox_overlap(ref(:),s);
    rel.reference = double(rel.reference);
end


% ---
function rel=updatedesign(rel,ds,tl,tc)

tc = tc-repmat(mean(tc),size(tc,1),1);
tc = tc./repmat(std(tc),size(tc,1),1);
st = size(tc);
sd = size(ds);
i = 1;
while (isfield(rel,sprintf('design%d',i)))
    rel = rmfield(rel,sprintf('design%d',i));
    i = i+1;
end
if (sd(2)~=0)
    nds = zeros(length(tl),sd(2));
    for i=1:sd(2)
        nds(:,i) = interp1(linspace(tl(1),tl(end),sd(1)),ds(:,i),tl)';
    end
    nds = nds-repmat(mean(nds),size(nds,1),1);
    nds = nds./repmat(std(nds),size(nds,1),1);
    for i=1:sd(2)
        rel.(sprintf('design%d',i)) = double(abs(nds(:,i)'*tc)/(st(1)-1));
    end
end


% --- Executes on button press in export_data.
function export_data_Callback(hObject,eventdata,handles)

l = length(handles.mfbss.pre_name);
if (l>0)
    pl = length(handles.mfbss.pre_name);
    f = mat2cell(char(ones(1,2*pl-1)*'_'),1,ones(1,2*pl-1));
    f(1:2:(2*pl-1)) = handles.mfbss.pre_name;
    f = [reshape(char(f)',1,[]) '.nii'];
else
    f = [];
end
handles.filenames = mfbox_databackend('export', ...
    {handles.mfbss.X,handles.mfbss.mask,handles.mfbss.grid},handles.private,f);

guidata(hObject,handles);


% --- Executes on button press in run_pre.
function run_pre_Callback(hObject,eventdata,handles)

% returns content of listbox 'algo_preprocess' as cell array.
contents = get(handles.algo_preprocess,'String');
% returns selected item from algo_preprocess.
cmd_pre = {contents{get(handles.algo_preprocess,'Value')}};

handles.mfbss.X = handles.sequence;
dim = handles.sequence.dim;

% returns a dim-by-dim matrix of logical ones. 
handles.mfbss.mask = true(dim);

handles.mfbss.grid = mfbox_mkgrid(dim)';
handles.mfbss.timeline = 0:(handles.sequence.timesteps-1);

% identifies button to activate, fills in appropriate drop down boxes
handles = reset_views(handles,'plot_type',2);

for i=1:length(cmd_pre)
    cmd = cmd_pre{i};
    p = {};
    if (isfield(handles.mfbss.pre_params,cmd))
        p = handles.mfbss.pre_params.(cmd);
    end
    % str2func == @function
    % function, which will be called depends on 'cmd' argument, i.e.
    % cmd='remmean' => function 'mfbox_pre_remmeang.m'.
    cmd_func = str2func(sprintf('mfbox_pre_%s_run',cmd));
    
    % d:=data, m:=mask, g:=(data)grid, t:=timeline 
    [d,m,g,t,p,handles.private] = ...
        cmd_func(handles.mfbss.X,handles.mfbss.mask,handles.mfbss.grid, ...
        handles.mfbss.timeline,p,0,handles.private);
    if (isstruct(p)), handles.mfbss.pre_params.(cmd) = p;
    else return;
    end
end
handles.mfbss.pre_name = cmd_pre;

t = zeros(1,length(cmd_pre));
for i=1:length(cmd_pre), t(i) = handles.mfbss.pre_params.(cmd_pre{i}).priority; end
[d,s] = sort(t);

for i=1:length(cmd_pre)
    cmd = cmd_pre{s(i)};
    cmd_func = str2func(sprintf('mfbox_pre_%s_run',cmd));
    [handles.mfbss.X,handles.mfbss.mask,handles.mfbss.grid, ...
    handles.mfbss.timeline,handles.mfbss.pre_params.(cmd)] = ...
        cmd_func(handles.mfbss.X,handles.mfbss.mask,handles.mfbss.grid, ...
        handles.mfbss.timeline,handles.mfbss.pre_params.(cmd),2, ...
        handles.private);
end

handles.mfbss.A = []; handles.mfbss.W = []; handles.mfbss.S = struct();
handles.mfbss.ppA = []; handles.mfbss.ppW = []; handles.mfbss.ppS = struct();
if (isfield(handles.mfbss,'extraplot')), handles.mfbss = rmfield(handles.mfbss,'extraplot'); end

handles = reset_views(handles);

guidata(hObject,handles);


% --- Executes on button press in run_post.
function run_post_Callback(hObject,eventdata,handles)

contents = get(handles.algo_postprocess,'String');
cmd_pos = contents{get(handles.algo_postprocess,'Value')};

p = {};
if (isfield(handles.mfbss.pos_params,cmd_pos))
    p = handles.mfbss.pos_params.(cmd_pos);
end
cmd_func = str2func(sprintf('mfbox_pos_%s_run',cmd_pos));
rel = struct();
if (isempty(handles.mfbss.ppA))
    [handles.mfbss.ppA,handles.mfbss.ppW,handles.mfbss.ppS, ...
        p,rel] = cmd_func(handles.mfbss.A, ...
        handles.mfbss.W,handles.mfbss.S, ...
        {handles.mfbss.X,handles.mfbss.grid,handles.mfbss.mask, ...
            handles.mfbss.timeline,handles.mfbss.design,handles.mfbss.reference},p);
    if (isstruct(p)), handles.mfbss.pos_params.(cmd_pos) = p;
    else return;
    end
else
    [handles.mfbss.ppA,handles.mfbss.ppW,handles.mfbss.ppS, ...
        p,rel] = cmd_func( ...
        handles.mfbss.ppA,handles.mfbss.ppW,handles.mfbss.ppS, ...
        {handles.mfbss.X,handles.mfbss.grid,handles.mfbss.mask,handles.mfbss.timeline, ...
            handles.mfbss.design,handles.mfbss.reference},p);
    if (isstruct(p)), handles.mfbss.pos_params.(cmd_pos) = p;
    else return;
    end
end
l = length(handles.mfbss.pos_name);
handles.mfbss.pos_name{l+1} = cmd_pos;

s = [size(handles.mfbss.ppS.dat,1),size(handles.mfbss.ppS.map,2)];
S = zeros(s);
for i=1:s(2)
    j = unique(handles.mfbss.ppS.map(:,i));
    S(:,i) = sum(handles.mfbss.ppS.dat(:,j),2)/length(j);
end

handles.mfbss.ppcrosstalk = updatecrosstalk(handles.mfbss.ppA,S,{1:s(2)});

handles.mfbss.ppreliability = updatereliability(struct(),handles.mfbss.ppA,S);

handles.mfbss.ppreliability = updatedesign(handles.mfbss.ppreliability, ...
    handles.mfbss.design,handles.mfbss.timeline,handles.mfbss.ppA);

handles.mfbss.ppreliability = updatereference(handles.mfbss.ppreliability, ...
    handles.mfbss.reference,S,handles.mfbss.grid(:,handles.mfbss.ppS.mask));

v = fieldnames(rel);
for i=1:length(v)
    handles.mfbss.ppreliability.(v{i}) = rel.(v{i});
end
v = fieldnames(handles.mfbss.ppreliability);
for i=1:length(v)
    if (isempty(handles.mfbss.ppreliability.(v{i})))
        handles.mfbss.ppreliability = rmfield(handles.mfbss.ppreliability,v{i});
    end
end

handles = reset_views(handles);

guidata(hObject,handles);


% --- Executes on button press in clear_post.
function clear_post_Callback(hObject,eventdata,handles)

handles.mfbss.ppA = [];
handles.mfbss.ppW = [];
handles.mfbss.ppS = struct();
handles.mfbss.pos_name = {};

handles = reset_views(handles);

guidata(hObject,handles);


% --- Executes on selection change in sort_comp.
function sort_comp_Callback(hObject,eventdata,handles)

contents = get(hObject,'String');
v = contents{get(hObject,'Value')};